{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T21:12:55Z","timestamp":1687468375991},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2018,9,19]],"date-time":"2018-09-19T00:00:00Z","timestamp":1537315200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Max Planck Institute of Immunobiology and Epigenetics"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>This paper presents Parkour, a software package for sample processing and quality management of next generation sequencing data and samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Starting with user requests, Parkour allows tracking and assessing samples based on predefined quality criteria through different stages of the sample preparation workflow. Ideally suited for academic core laboratories, the software aims to maximize efficiency and reduce turnaround time by intelligent sample grouping and a clear assignment of staff to work units. Tools for automated invoicing, interactive statistics on facility usage and simple report generation minimize administrative tasks. Provided as a web application, Parkour is a convenient tool for both deep sequencing service users and laboratory personal. A set of web APIs allow coordinated information sharing with local and remote bioinformaticians. The flexible structure allows workflow customization and simple addition of new features as well as the expansion to other domains.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code and documentation are available at https:\/\/github.com\/maxplanck-ie\/parkour.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty820","type":"journal-article","created":{"date-parts":[[2018,9,18]],"date-time":"2018-09-18T19:17:00Z","timestamp":1537298220000},"page":"1422-1424","source":"Crossref","is-referenced-by-count":4,"title":["Parkour LIMS: high-quality sample preparation in next generation sequencing"],"prefix":"10.1093","volume":"35","author":[{"given":"E","family":"Anatskiy","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany"}]},{"given":"D P","family":"Ryan","sequence":"additional","affiliation":[{"name":"Bioinformatics Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany"}]},{"given":"B A","family":"Gr\u00fcning","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany"},{"name":"Bioinformatics Group, Center for Biological Systems Analysis (ZBSA), University Freiburg, Freiburg, Germany"}]},{"given":"L","family":"Arrigoni","sequence":"additional","affiliation":[{"name":"Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany"}]},{"given":"T","family":"Manke","sequence":"additional","affiliation":[{"name":"Bioinformatics Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany"}]},{"given":"U","family":"B\u00f6nisch","sequence":"additional","affiliation":[{"name":"Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,9,19]]},"reference":[{"key":"2023012808251881200_bty820-B1","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses","volume":"44","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023012808251881200_bty820-B2","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1093\/bioinformatics\/btv606","article-title":"OpenBIS ELN-LIMS: an open-source database for academic laboratories","volume":"32","author":"Barillari","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012808251881200_bty820-B3","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1515\/jib-2015-274","article-title":"OpenLabNotes\u2014an electronic laboratory notebook extension for OpenLabFramework","volume":"., 12","author":"List","year":"2015","journal-title":"J. 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